Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.16.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.44888	0.656
27DAP/17DAP	1.6881	0.312
39DAP/27DAP	2.77504	0.329
41DAP/39DAP	1.8854	0.597
42DAP/41DAP	0.93663	1
43DAP/42DAP	1.41735	1
47DAP/43DAP	0.17989	0.038
52DAP/47DAP	1.08117	0.973
57DAP/52DAP	0.95969	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.61725	0.025
17DAP/reference	0.64125	0.01
27DAP/reference	0.92003	0.314
39DAP/reference	0.63324	0.015
41DAP/reference	0.79576	0.201
42DAP/reference	2.06218	0.002
43DAP/reference	0.69918	0.026
47DAP/reference	0.76276	0.004
52DAP/reference	0.80133	0.131
57DAP/reference	1.07339	0.355

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87999	0.336
27DAP/17DAP	1.14667	0.852
39DAP/27DAP	5.44029	0.039
41DAP/39DAP	5.3905	0.005
42DAP/41DAP	0.53034	0.007
43DAP/42DAP	0.28133	0.014
47DAP/43DAP	1.2019	0.286
52DAP/47DAP	1.47749	0.919
57DAP/52DAP	0.50275	0.187
57DAP/7DAP	1.29083	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60091	0.063
17DAP/reference	1.76286	0.162
27DAP/reference	2.18146	0.107
39DAP/reference	2.29548	0.081
41DAP/reference	0.92777	0.271
42DAP/reference	2.14177	0.233
43DAP/reference	1.07404	0.802
47DAP/reference	2.2749	0.083
52DAP/reference	1.92186	0.02
57DAP/reference	2.73343	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60213	0.014
17DAP/reference	0.8029	0.068
27DAP/reference	0.88765	0.188
39DAP/reference	2.28622	0.026
41DAP/reference	1.60407	0.012
42DAP/reference	1.82528	0.133
43DAP/reference	3.35329	0.097
47DAP/reference	3.89598	0.011
52DAP/reference	1.34407	0.057
57DAP/reference	5.01679	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97946	0.391
17DAP/reference	1.39355	0.675
27DAP/reference	0.84487	0.05
39DAP/reference	1.5252	0.052
41DAP/reference	2.05859	0.02
42DAP/reference	0.84439	0.22
43DAP/reference	0.72214	0.023
47DAP/reference	0.58151	0.004
52DAP/reference	0.65291	0.081
57DAP/reference	0.88952	0.18

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.49811	0.966
26DAP/20DAP	1.02361	1
34DAP/26DAP	0.80651	0.462
51DAP/34DAP	0.75908	0.188
52DAP/51DAP	1.2211	0.565
53DAP/52DAP	1.23248	0.819
55DAP/53DAP	0.90392	0.604
57DAP/55DAP	0.90693	0.694
62DAP/57DAP	0.98076	0.871
68DAP/62DAP	1.45863	0.44
68DAP/14DAP	0.90481	1

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.33003	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	15.1261	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.35549	0.224
Mature Eggplant/Ripe Tomato	0.11615	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.49323
1-1-2/M82	1.60059	1
12-2/M82	1.21698	1
12-4/M82	0.9984	1
1-3/M82	2.50656
2-1-1/M82	0.80408
2-1/M82	5.13945	0.345
2-6/M82	1.67218	0.355
3-2/M82	6.57588
4-1-1/M82	4.07707	0.657
4-1/M82	2.44852
4-3-2/M82	6.79483	0.241
4-3/M82	0.63605	0.72
5-3/M82	1.63516	0.455
6-2/M82	14.8099	0.253
6-3/M82	1.16998	1
7-1/M82	0.17618	0.509
7-2/M82	2.03468	0.291
9-3-2/M82	3.15183

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.77193	0.853

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00482	0.921
DC3000/delta hrp 6h	0.68212
DC3000/delta hrp 12h	1.15251	1
DC3000/delta hrp 24h	3.07983	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.05469	0.042
DC3000 delta B/DC3000 delta AB	4.54159	0.021

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.97756	0.254
Exp 36h	1.65315	1
Exp 60h	2.61386	0.226

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.01326	1
Var 0h	1.42395	0.936
Var 12h I row2-row1	1.00253	1
Var 12h NI row2-row1	3.0176	0.224
Var 36h I row2-row1	1.3247	1
Var 36h NI row2-row1	0.55517	0.522
Var 60h I row2-row1	0.94433	0.832
Var 60h NI row2-row1	0.62051	0.431
Time course 0hI-0hNI	1.94631	0.662
Time course 12hI-12hNI	2.0845	0.445
Time course 36hI-36hNI	11.1506	0.004
Time course 60hI-60hNI	201.269	0.008

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.37791	0.246
transgenic ySAMdc/azygous control (breaker)	0.52588	0.142
transgenic ySAMdc/azygous control (red)	1.01537	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95275	0.128

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.08654	0.238

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05839	1
Manapal/WT (break)	0.38514	0.333
Manapal/WT (red)	0.38744	0.274